Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 14 of 27
Found at i:2106355 original size:24 final size:24
Alignment explanation
Indices: 2106304--2106369 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
2106294 ATTTGTATTT
2106304 ATATTATT--TTTTATAT-TTAAA
1 ATATTATTAATTTTATATATTAAA
2106325 ATATTA-TAATTTTATATATTAATA
1 ATATTATTAATTTTATATATTAA-A
* *
2106349 ATTTTATTTTATTTTATATAT
1 ATATTA-TTAATTTTATATAT
2106370 ATTTTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 8 0.22
23 4 0.11
24 6 0.16
26 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTATTAATTTTATATATTAAA
Found at i:2106417 original size:11 final size:11
Alignment explanation
Indices: 2106403--2106463 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
2106393 TATTATGTAC
2106403 ATATTATTTTT
1 ATATTATTTTT
2106414 ATATTATGTTTT
1 ATATTAT-TTTT
*
2106426 A-AATATTTTT
1 ATATTATTTTT
*
2106436 ATAAATAATATATTT
1 AT--AT--TATTTTT
2106451 ATATTATTTTT
1 ATATTATTTTT
2106462 AT
1 AT
2106464 GTTTAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
10 5 0.12
11 19 0.47
12 5 0.12
13 3 0.08
15 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:2107344 original size:16 final size:17
Alignment explanation
Indices: 2107317--2107357 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2107307 AATTTGAAAT
2107317 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
2107332 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
2107349 AAATTTTAT
1 AAATTTTAT
2107358 GAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:2107803 original size:16 final size:17
Alignment explanation
Indices: 2107777--2107814 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2107767 ATTTGAATCA
*
2107777 ATTTTTAAATTTAAATT
1 ATTTTTAAATTTAAAGT
*
2107794 ATTTTT-AATTTTAAGT
1 ATTTTTAAATTTAAAGT
2107810 ATTTT
1 ATTTT
2107815 AAGCTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTTAAATTTAAAGT
Found at i:2113876 original size:2 final size:2
Alignment explanation
Indices: 2113869--2113896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2113859 TACATTAAAC
2113869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2113897 GCAAGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2118153 original size:23 final size:23
Alignment explanation
Indices: 2118126--2118169 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2118116 ATTACTACAT
2118126 ATTTA-AT-TAATCATAAGTTAAAA
1 ATTTAGATATAATC-TAA-TTAAAA
2118149 ATTTAGATATAATCTAATTAA
1 ATTTAGATATAATCTAATTAA
2118170 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 5 0.26
25 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (23 bp):
ATTTAGATATAATCTAATTAAAA
Found at i:2120533 original size:19 final size:20
Alignment explanation
Indices: 2120509--2120546 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2120499 TTAAACAAAA
2120509 AATAAAA-TTTGTTATATCT
1 AATAAAAGTTTGTTATATCT
*
2120528 AATAAAAGTTTTTTATATC
1 AATAAAAGTTTGTTATATC
2120547 ATATAGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
AATAAAAGTTTGTTATATCT
Found at i:2120837 original size:5 final size:5
Alignment explanation
Indices: 2120827--2120859 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2120817 ATATAAATAA
*
2120827 TTATT TTATT TTATT GTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTATT TTA
2120860 ATACATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:2121464 original size:17 final size:17
Alignment explanation
Indices: 2121442--2121478 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2121432 AATTATTTTT
2121442 TATATATATAAAT-TAAA
1 TATATAT-TAAATATAAA
2121459 TATATATTAAATATAAA
1 TATATATTAAATATAAA
2121476 TAT
1 TAT
2121479 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATATTAAATATAAA
Found at i:2121467 original size:11 final size:11
Alignment explanation
Indices: 2121447--2121476 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2121437 TTTTTTATAT
2121447 ATATAAATTAA
1 ATATAAATTAA
*
2121458 ATATATATTAA
1 ATATAAATTAA
2121469 ATATAAAT
1 ATATAAAT
2121477 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAAATTAA
Found at i:2122377 original size:21 final size:22
Alignment explanation
Indices: 2122353--2122397 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2122343 TTTTTAATTT
*
2122353 AAATTAGA-TATGAAATTAAAA
1 AAATTAGATTATGAAAATAAAA
* *
2122374 AAATTATATTATTAAAATAAAA
1 AAATTAGATTATGAAAATAAAA
2122396 AA
1 AA
2122398 TTATTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATTAGATTATGAAAATAAAA
Found at i:2122409 original size:21 final size:21
Alignment explanation
Indices: 2122371--2122410 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2122361 TATGAAATTA
*
2122371 AAAAAATTATATTATTAAAAT
1 AAAAAATTATAATATTAAAAT
2122392 AAAAAATTATTAAT-TTAAA
1 AAAAAATTA-TAATATTAAA
2122411 GTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATTATAATATTAAAAT
Found at i:2122457 original size:17 final size:17
Alignment explanation
Indices: 2122435--2122467 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2122425 AGTCAATCCC
2122435 TAAA-TTTAAATTATTTG
1 TAAATTTTAAA-TATTTG
2122452 TAAATTTTAAATATTT
1 TAAATTTTAAATATTT
2122468 TAAGCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TAAATTTTAAATATTTG
Found at i:2127352 original size:2 final size:2
Alignment explanation
Indices: 2127336--2127383 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2127326 CCTCGTAGAA
*
2127336 AT AT GT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2127377 AT AT AT A
1 AT AT AT A
2127384 ATTCCTCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2127864 original size:2 final size:2
Alignment explanation
Indices: 2127857--2127887 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2127847 CCTAATGATC
2127857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2127888 CAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2128448 original size:16 final size:16
Alignment explanation
Indices: 2128427--2128460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2128417 TTTATTAAAC
2128427 AATTAAAATAATAATT
1 AATTAAAATAATAATT
* *
2128443 AATTAAATTAATTATT
1 AATTAAAATAATAATT
2128459 AA
1 AA
2128461 AATCATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAATAATAATT
Found at i:2128972 original size:7 final size:8
Alignment explanation
Indices: 2128947--2128971 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2128937 ATTACTTATA
2128947 TTATTTTT
1 TTATTTTT
2128955 TTATTTTT
1 TTATTTTT
2128963 TTATTTTT
1 TTATTTTT
2128971 T
1 T
2128972 ACTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:2128977 original size:19 final size:19
Alignment explanation
Indices: 2128955--2128991 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2128945 TATTATTTTT
**
2128955 TTATTTTTTTATTTTTTAC
1 TTATTTTTCCATTTTTTAC
2128974 TTATTTTTCCATTTTTTA
1 TTATTTTTCCATTTTTTA
2128992 AAAGTTTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATTTTTCCATTTTTTAC
Found at i:2128980 original size:16 final size:17
Alignment explanation
Indices: 2128938--2128980 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2128928 TACTTATATA
*
2128938 TTACTTATATTATTTTT
1 TTACTTATTTTATTTTT
*
2128955 TTA-TTTTTTTA-TTTT
1 TTACTTATTTTATTTTT
2128970 TTACTTATTTT
1 TTACTTATTTT
2128981 TCCATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.32
16 12 0.55
17 3 0.14
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTACTTATTTTATTTTT
Found at i:2129306 original size:2 final size:2
Alignment explanation
Indices: 2129294--2129363 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
2129284 GCCCTATTTA
* * * * * *
2129294 AT AT AT A- AT AT AT AT GT GT GT GT AT AA AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2129335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2129364 CACACATACA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2131886 original size:10 final size:10
Alignment explanation
Indices: 2131866--2131894 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2131856 TTATTATTAT
2131866 AAAAATT-AA
1 AAAAATTAAA
2131875 AAAAATTAAA
1 AAAAATTAAA
2131885 AAAAATTAAA
1 AAAAATTAAA
2131895 TGAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:2131900 original size:10 final size:9
Alignment explanation
Indices: 2131861--2131894 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2131851 TTAATTTATT
*
2131861 ATTATAAAA
1 ATTAAAAAA
2131870 ATTAAAAAA
1 ATTAAAAAA
2131879 ATTAAAAAAA
1 ATT-AAAAAA
2131889 ATTAAA
1 ATTAAA
2131895 TGAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:2132336 original size:23 final size:24
Alignment explanation
Indices: 2132293--2132339 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2132283 GTTGTGATAA
* *
2132293 AATATAATAATATGATATAAATAT
1 AATATAATAAAATAATATAAATAT
2132317 AATATAA-AAAATAATATAAATAT
1 AATATAATAAAATAATATAAATAT
2132340 TTATTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
AATATAATAAAATAATATAAATAT
Found at i:2132353 original size:36 final size:37
Alignment explanation
Indices: 2132313--2132391 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 37
2132303 TATGATATAA
* *
2132313 ATATAATATAAAAAATAATATAAATATT-TATTTAAT
1 ATATAATATAAAAAATAATAAAAATATTAAATTTAAT
*
2132349 ATAT-A-AT-AAAAATAATAAAAATATTAAATTTTAT
1 ATATAATATAAAAAATAATAAAAATATTAAATTTAAT
2132383 ATA-AATATA
1 ATATAATATA
2132392 TAATATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
33 17 0.47
34 12 0.33
35 3 0.08
36 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
ATATAATATAAAAAATAATAAAAATATTAAATTTAAT
Found at i:2132386 original size:20 final size:21
Alignment explanation
Indices: 2132363--2132406 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2132353 AATAAAAATA
2132363 ATAAAAATATTAA-A-TTTTAT
1 ATAAAAATA-TAATATTTTTAT
*
2132383 ATAAATATATAATATTTTTAT
1 ATAAAAATATAATATTTTTAT
2132404 ATA
1 ATA
2132407 TTATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.43
21 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAAAATATAATATTTTTAT
Found at i:2132427 original size:13 final size:14
Alignment explanation
Indices: 2132411--2132444 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2132401 TATATATTAT
2132411 TATAAAATAAA-AA
1 TATAAAATAAATAA
2132424 TATATAAATAAATAA
1 TATA-AAATAAATAA
2132439 TATAAA
1 TATAAA
2132445 TATACGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TATAAAATAAATAA
Found at i:2132538 original size:10 final size:10
Alignment explanation
Indices: 2132523--2132556 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2132513 CATTACTTTT
2132523 ATTAATTTAA
1 ATTAATTTAA
2132533 ATTAATTTAA
1 ATTAATTTAA
* *
2132543 TTTGATTTAA
1 ATTAATTTAA
2132553 ATTA
1 ATTA
2132557 TTATTTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:2132954 original size:17 final size:17
Alignment explanation
Indices: 2132894--2132957 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
2132884 CCGATAATTT
2132894 TAAATAT-AATATAAAA
1 TAAATATAAATATAAAA
*
2132910 TATAATACAGTAA-A-AAAA
1 TA-AATATA--AATATAAAA
*
2132928 TTAATATAAATATAAAA
1 TAAATATAAATATAAAA
2132945 TAAATATAAATAT
1 TAAATATAAATAT
2132958 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
15 2 0.05
16 3 0.08
17 25 0.66
18 5 0.13
19 1 0.03
20 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAATATAAATATAAAA
Found at i:2133121 original size:18 final size:19
Alignment explanation
Indices: 2133098--2133133 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2133088 GTTTATATTG
2133098 ATAATTTTAAATT-TTTTA
1 ATAATTTTAAATTATTTTA
2133116 ATAATTTTAAATTATTTT
1 ATAATTTTAAATTATTTT
2133134 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATAATTTTAAATTATTTTA
Found at i:2133173 original size:21 final size:22
Alignment explanation
Indices: 2133126--2133173 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2133116 ATAATTTTAA
* * *
2133126 ATTATTTTTATATATATTATTT
1 ATTATTTTTATATAAAATATAT
*
2133148 TTTATTTTTA-ATAAAATATAT
1 ATTATTTTTATATAAAATATAT
2133169 ATTAT
1 ATTAT
2133174 ATAATTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTTTATATAAAATATAT
Found at i:2133262 original size:21 final size:20
Alignment explanation
Indices: 2133235--2133302 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
2133225 TAATTTTTTA
2133235 AAAATATTTAATATAAA-AAAT
1 AAAATA-TTAA-ATAAATAAAT
*
2133256 TAAATATTAAATAAATAAAT
1 AAAATATTAAATAAATAAAT
* * *
2133276 AAAAT-TAAAATATAT-GAT
1 AAAATATTAAATAAATAAAT
2133294 AAAATATTA
1 AAAATATTA
2133303 TTAATCAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.18
19 15 0.38
20 12 0.31
21 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAATATTAAATAAATAAAT
Found at i:2134514 original size:15 final size:15
Alignment explanation
Indices: 2134494--2134542 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2134484 AAATATAAAT
*
2134494 AATAATTATGAATAA
1 AATAATTATAAATAA
2134509 AATAATTATAAATAA
1 AATAATTATAAATAA
*
2134524 TATTAA-TATAAA-AA
1 -AATAATTATAAATAA
2134538 AATAA
1 AATAA
2134543 AAATATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 2 0.07
15 20 0.67
16 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATTATAAATAA
Found at i:2134593 original size:11 final size:12
Alignment explanation
Indices: 2134562--2134607 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
2134552 AATATTAATT
*
2134562 AATATTTAATAA
1 AATATTTTATAA
2134574 AATTATTTTAT-A
1 AA-TATTTTATAA
2134586 AATATTTT-TAA
1 AATATTTTATAA
2134597 AATATATTTAT
1 AATAT-TTTAT
2134608 TTTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 1 0.03
11 12 0.41
12 8 0.28
13 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTTTATAA
Found at i:2134606 original size:23 final size:24
Alignment explanation
Indices: 2134547--2134607 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
2134537 AAATAAAAAT
* *
2134547 ATAAAA-ATATTAATTAATATTTA
1 ATAAAATATATTTATAAATATTTA
2134570 ATAAAAT-TATTTTATAAATATTT-
1 ATAAAATATA-TTTATAAATATTTA
*
2134593 TTAAAATATATTTAT
1 ATAAAATATATTTAT
2134608 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAAAATATATTTATAAATATTTA
Found at i:2134645 original size:24 final size:24
Alignment explanation
Indices: 2134618--2134664 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2134608 TTTTTAAATT
2134618 TAAAAAATAA-ATAAAGTATTATTA
1 TAAAAAATAATATAAAGT-TTATTA
* *
2134642 TAAATAATAATTTAAAGTTTATT
1 TAAAAAATAATATAAAGTTTATT
2134665 CTTAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAAAAATAATATAAAGTTTATTA
Found at i:2144771 original size:16 final size:16
Alignment explanation
Indices: 2144750--2144782 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2144740 AATGAAGCGG
*
2144750 AAAAAGACAAAAAAGA
1 AAAAAGAAAAAAAAGA
2144766 AAAAAGAAAAAAAAGA
1 AAAAAGAAAAAAAAGA
2144782 A
1 A
2144783 CTCCTTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:2146602 original size:16 final size:17
Alignment explanation
Indices: 2146563--2146602 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2146553 AATATTTATA
2146563 AAAATTT-TAATTAAAT
1 AAAATTTATAATTAAAT
2146579 AAAA-TTATAATT-AAT
1 AAAATTTATAATTAAAT
2146594 AAAATTTAT
1 AAAATTTAT
2146603 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTTATAATTAAAT
Found at i:2146897 original size:31 final size:31
Alignment explanation
Indices: 2146862--2146961 Score: 121
Period size: 31 Copynumber: 3.2 Consensus size: 31
2146852 TAAATATATT
2146862 AAAATATAGATAAACTAATAATTAATATGTA
1 AAAATATAGATAAACTAATAATTAATATGTA
* * * * *
2146893 AAAATTTATATAACACGT-ATATATGAATATATT
1 AAAATATAGATAA-AC-TAATA-ATTAATATGTA
2146926 AAAATATAGATAAACTAATAATTAATATGTA
1 AAAATATAGATAAACTAATAATTAATATGTA
2146957 AAAAT
1 AAAAT
2146962 TTATTTTACT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
31 25 0.45
32 10 0.18
33 20 0.36
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (31 bp):
AAAATATAGATAAACTAATAATTAATATGTA
Found at i:2146915 original size:64 final size:64
Alignment explanation
Indices: 2146836--2146965 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
2146826 AATAACATGA
*
2146836 ATATAACATGGATATATAAATATATTAAAATATAGATAAACTAATAATTAATATGTAAAAATTT
1 ATATAACACGGATATATAAATATATTAAAATATAGATAAACTAATAATTAATATGTAAAAATTT
* *
2146900 ATATAACACGTATATATGAATATATTAAAATATAGATAAACTAATAATTAATATGTAAAAATTT
1 ATATAACACGGATATATAAATATATTAAAATATAGATAAACTAATAATTAATATGTAAAAATTT
2146964 AT
1 AT
2146966 TTTACTTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (64 bp):
ATATAACACGGATATATAAATATATTAAAATATAGATAAACTAATAATTAATATGTAAAAATTT
Found at i:2147190 original size:11 final size:10
Alignment explanation
Indices: 2147174--2147208 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
2147164 AATGCATAAA
2147174 TTTTTCTCTTT
1 TTTTTCT-TTT
2147185 TTTTTCTTTT
1 TTTTTCTTTT
2147195 CTTTTTCTTTT
1 -TTTTTCTTTT
2147206 TTT
1 TTT
2147209 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2147617 original size:12 final size:13
Alignment explanation
Indices: 2147585--2147631 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
2147575 GAATATACGA
*
2147585 AATATAAAAATAT
1 AATATAAAAAAAT
*
2147598 AACATAAAAAAAT
1 AATATAAAAAAAT
*
2147611 AAT-T-AAAACAT
1 AATATAAAAAAAT
2147622 AATATAAAAA
1 AATATAAAAA
2147632 TAAATGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 9 0.32
12 2 0.07
13 17 0.61
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATAAAAAAAT
Found at i:2147812 original size:22 final size:22
Alignment explanation
Indices: 2147764--2147812 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
2147754 TTTCTCTCTA
2147764 TCTC-TTTTTCTTTCTTTTCTT
1 TCTCTTTTTTCTTTCTTTTCTT
*
2147785 TGCTCTTTTTTTTTTCTATTT-TT
1 T-CTCTTTTTTCTTTCT-TTTCTT
2147808 TCTCT
1 TCTCT
2147813 CTCATAGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 7 0.29
23 13 0.54
24 3 0.12
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (22 bp):
TCTCTTTTTTCTTTCTTTTCTT
Found at i:2147814 original size:24 final size:24
Alignment explanation
Indices: 2147742--2147814 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 24
2147732 AATACATTAA
2147742 CTTTTTCTTTTATTTCTCTCTATCT
1 CTTTTTCTTTT-TTTCTCTCTATCT
*
2147767 CTTTTTCTTTCTTTTCTTTGCTCT-TTT
1 CTTTTTCTTT-TTTTC--T-CTCTATCT
*
2147794 TTTTTTCTATTTTTTCTCTCT
1 CTTTTTCT-TTTTTTCTCTCT
2147815 CATAGATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
24 4 0.10
25 15 0.37
26 1 0.02
27 15 0.37
28 6 0.15
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73
Consensus pattern (24 bp):
CTTTTTCTTTTTTTCTCTCTATCT
Found at i:2147991 original size:23 final size:21
Alignment explanation
Indices: 2147956--2147999 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2147946 ATACGAATAT
*
2147956 ATTAAGATATAAATAAATTTATA
1 ATTAACATAT-AA-AAATTTATA
*
2147979 ATTAACATGTAAAAATTTATA
1 ATTAACATATAAAAATTTATA
2148000 TAAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
ATTAACATATAAAAATTTATA
Found at i:2148061 original size:13 final size:13
Alignment explanation
Indices: 2148022--2148063 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2148012 ATTTTAATAA
2148022 TATAAAAAATA-T
1 TATAAAAAATATT
*
2148034 CATAAACATAATATT
1 TATAAA-A-AATATT
2148049 TATAAAAAATATT
1 TATAAAAAATATT
2148062 TA
1 TA
2148064 AAATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 5 0.20
15 6 0.24
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAAAAAATATT
Found at i:2148095 original size:17 final size:17
Alignment explanation
Indices: 2148073--2148183 Score: 58
Period size: 16 Copynumber: 6.6 Consensus size: 17
2148063 AAAATATAAT
*
2148073 ATAAAAATAATATGTAC
1 ATAAAAATAATATGTAA
* *
2148090 AT-AAAATAA-ATATAT
1 ATAAAAATAATATGTAA
2148105 ATAAAAATATATATG-AA
1 ATAAAAATA-ATATGTAA
2148122 ATAAAAA-AATTAT-TAA
1 ATAAAAATAA-TATGTAA
*
2148138 TATATAAAA-AAT-T-TAT
1 -ATA-AAAATAATATGTAA
*
2148154 ATAAAAATATAATATTTTAA
1 AT-AAAA-ATAATA-TGTAA
2148174 ATAAAAATAA
1 ATAAAAATAA
2148184 AAATATTAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
15 12 0.16
16 24 0.32
17 18 0.24
18 12 0.16
19 5 0.07
20 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAAAATAATATGTAA
Found at i:2148111 original size:32 final size:32
Alignment explanation
Indices: 2148063--2148146 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 32
2148053 AAAAATATTT
*
2148063 AAAATATAATATAAAAATA-ATATGTACATAAA
1 AAAATATAATATAAAAATATATATG-AAATAAA
2148095 ATAAATAT-ATATAAAAATATATATGAAATAAA
1 A-AAATATAATATAAAAATATATATGAAATAAA
2148127 AAAATTATTAATATATAAAA
1 AAAA-TA-TAATATA-AAAA
2148147 AATTTATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
31 3 0.07
32 21 0.47
33 12 0.27
34 5 0.11
35 4 0.09
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (32 bp):
AAAATATAATATAAAAATATATATGAAATAAA
Found at i:2148126 original size:27 final size:27
Alignment explanation
Indices: 2148016--2148124 Score: 84
Period size: 27 Copynumber: 4.0 Consensus size: 27
2148006 TATTTTATTT
*
2148016 TAATA-ATATAAAAAATATCAT-AAACA
1 TAATATATATAAAAAATAT-ATAAAATA
* *
2148042 TAATATTTATAAAAAATATTTAAAATA
1 TAATATATATAAAAAATATATAAAATA
*
2148069 TAATATA-A-AAATAATATGTACATAAAATA
1 TAATATATATAAA-AA-A--TATATAAAATA
*
2148098 -AATATATATAAAAATATATATGAAATA
1 TAATATATATAAAAA-ATATATAAAATA
2148125 AAAAAATTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.04
26 9 0.13
27 32 0.48
28 6 0.09
29 14 0.21
30 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (27 bp):
TAATATATATAAAAAATATATAAAATA
Found at i:2148126 original size:49 final size:52
Alignment explanation
Indices: 2148073--2148199 Score: 131
Period size: 49 Copynumber: 2.5 Consensus size: 52
2148063 AAAATATAAT
*
2148073 ATAAAAATAA-TATGTACATA-A-AATAAATATATATAAAAATAT-ATA-TGAA
1 ATAAAAATAATTAT-TA-ATATATAAAAAATATATATAAAAATATAATATTGAA
* *
2148122 ATAAAAA-AATTATTAATATATAAAAAATTTATATAAAAATATAATATTTTAA
1 ATAAAAATAATTATTAATATATAAAAAATATATATAAAAATATAATA-TTGAA
*
2148174 ATAAAAATAAAAATATTAATATATAA
1 ATAAAAAT--AATTATTAATATATAA
2148200 TTTTTTTTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
47 3 0.05
48 5 0.08
49 29 0.45
50 3 0.05
52 10 0.15
55 15 0.23
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (52 bp):
ATAAAAATAATTATTAATATATAAAAAATATATATAAAAATATAATATTGAA
Found at i:2148144 original size:19 final size:18
Alignment explanation
Indices: 2148122--2148199 Score: 52
Period size: 19 Copynumber: 4.2 Consensus size: 18
2148112 TATATATGAA
2148122 ATAAAAAAATTATTAATAT
1 ATAAAAAAATTATTAA-AT
* *
2148141 ATAAAAAATTTATATAAAA
1 ATAAAAAAATTAT-TAAAT
* *
2148160 AT-ATAATATT-TTAAAT
1 ATAAAAAAATTATTAAAT
* *
2148176 AAAAATAAAAATATTAATAT
1 ATAAA-AAAATTATTAA-AT
2148196 ATAA
1 ATAA
2148200 TTTTTTTTCT
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
16 5 0.12
17 2 0.05
18 9 0.21
19 19 0.44
20 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAAAAATTATTAAAT
Found at i:2148149 original size:26 final size:26
Alignment explanation
Indices: 2148110--2148199 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 26
2148100 TATATATAAA
**
2148110 AATATATATGAAATAA-AAAAATTATT
1 AATATATAAAAAATAATAAAAA-TATT
2148136 AATATATAAAAAATTTATATAAAAATA-T
1 AATATATAAAAAA--TA-ATAAAAATATT
*
2148164 AATATTTTAAATAAA-AATAAAAATATT
1 AATA-TATAAA-AAATAATAAAAATATT
2148191 AATATATAA
1 AATATATAA
2148200 TTTTTTTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
26 24 0.45
27 6 0.11
28 7 0.13
29 8 0.15
30 8 0.15
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (26 bp):
AATATATAAAAAATAATAAAAATATT
Found at i:2159549 original size:17 final size:17
Alignment explanation
Indices: 2159524--2159557 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2159514 CCGACTGAAT
2159524 GGTACGAGTAACACGAA
1 GGTACGAGTAACACGAA
*
2159541 GGTATGAGTAACACGAA
1 GGTACGAGTAACACGAA
2159558 TGCAGCTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (17 bp):
GGTACGAGTAACACGAA
Found at i:2163927 original size:3 final size:3
Alignment explanation
Indices: 2163919--2163974 Score: 60
Period size: 3 Copynumber: 17.7 Consensus size: 3
2163909 AAAGTCTTTA
*
2163919 ATT ATT ATTT ATTT ATTT ATAT ATT ATT ATT ATT ATT ATT ATT ATT AAT
1 ATT ATT A-TT A-TT A-TT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
2163968 ATT -TT AT
1 ATT ATT AT
2163975 GAGAAATACT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 32 0.67
4 14 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2171060 original size:11 final size:12
Alignment explanation
Indices: 2171039--2171077 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
2171029 TGCATAATAT
2171039 TATTATTTATGA
1 TATTATTTATGA
2171051 TATT-TTTATG-
1 TATTATTTATGA
2171061 TATTATTTATGA
1 TATTATTTATGA
*
2171073 GATTA
1 TATTA
2171078 AAAAAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.17
11 12 0.50
12 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (12 bp):
TATTATTTATGA
Found at i:2172156 original size:3 final size:3
Alignment explanation
Indices: 2172138--2172171 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2172128 GGATATGGAA
* *
2172138 GAT GGT GAT AAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
2172172 GGCCTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2177513 original size:2 final size:2
Alignment explanation
Indices: 2177506--2177534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2177496 TTGGCCAAAC
2177506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2177535 GACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2178833 original size:2 final size:2
Alignment explanation
Indices: 2178826--2178855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2178816 CCTTTCTTTC
2178826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2178856 GAATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2181053 original size:33 final size:33
Alignment explanation
Indices: 2181016--2181084 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
2181006 TTTTTATGTT
*
2181016 TATTTT-TAAATATTAAATATTAAATAT-TTTTTA
1 TATTTTATAAAT-TTAAA-ATTAAATATGATTTTA
*
2181049 TATTTTAATAAATTTATAATTAAATATGATTTTA
1 TATTTT-ATAAATTTAAAATTAAATATGATTTTA
2181083 TA
1 TA
2181085 AAATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 15 0.48
34 11 0.35
35 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
TATTTTATAAATTTAAAATTAAATATGATTTTA
Found at i:2181108 original size:16 final size:16
Alignment explanation
Indices: 2181089--2181121 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2181079 TTTATAAAAT
*
2181089 ATTTTATTTAAATTTA
1 ATTTGATTTAAATTTA
2181105 ATTTGATTTAAATTTA
1 ATTTGATTTAAATTTA
2181121 A
1 A
2181122 AATTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTGATTTAAATTTA
Found at i:2181202 original size:22 final size:22
Alignment explanation
Indices: 2181159--2181199 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2181149 AAATTCATAA
2181159 AATTTAAATATCAAATTTAATT
1 AATTTAAATATCAAATTTAATT
*
2181181 AATTTAAATA-CGAATTTAA
1 AATTTAAATATCAAATTTAA
2181200 ATTTAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTAAATATCAAATTTAATT
Found at i:2187376 original size:3 final size:3
Alignment explanation
Indices: 2187363--2187403 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
2187353 TTCACTGCAA
*
2187363 AAT AA- AAT AAT AAT GAT AAT AAT AA- AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2187404 TAGTATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2187388 original size:20 final size:20
Alignment explanation
Indices: 2187363--2187403 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2187353 TTCACTGCAA
*
2187363 AATAAAATAATAATGATAAT
1 AATAAAATAATAATAATAAT
2187383 AATAAAATAATAATAATAAT
1 AATAAAATAATAATAATAAT
2187403 A
1 A
2187404 TAGTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAAAATAATAATAATAAT
Found at i:2187391 original size:17 final size:17
Alignment explanation
Indices: 2187371--2187403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2187361 AAAATAAAAT
*
2187371 AATAATGATAATAATAA
1 AATAATAATAATAATAA
2187388 AATAATAATAATAATA
1 AATAATAATAATAATA
2187404 TAGTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:2191205 original size:24 final size:23
Alignment explanation
Indices: 2191173--2191221 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2191163 TAAAGTAAAA
*
2191173 TTTCTTATTCCT-TTTTCTGTTCTT
1 TTTCATATTCCTATTTT-T-TTCTT
*
2191197 TTTCATATTTCTATTTTTTTCTT
1 TTTCATATTCCTATTTTTTTCTT
2191220 TT
1 TT
2191222 GTTTTTCCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTCATATTCCTATTTTTTTCTT
Found at i:2192023 original size:17 final size:16
Alignment explanation
Indices: 2191997--2192030 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2191987 ATCGATGTAG
2191997 AATATAAATATATATTA
1 AATATAAATATAT-TTA
*
2192014 AATATGAATATATTTA
1 AATATAAATATATTTA
2192030 A
1 A
2192031 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATAAATATATTTA
Found at i:2192037 original size:21 final size:21
Alignment explanation
Indices: 2192011--2192051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2192001 TAAATATATA
2192011 TTAAATATGAATATATTTAAT
1 TTAAATATGAATATATTTAAT
* **
2192032 TTAAATTTTTATATATTTAA
1 TTAAATATGAATATATTTAA
2192052 AAATTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAAATATGAATATATTTAAT
Found at i:2192047 original size:23 final size:23
Alignment explanation
Indices: 2192021--2192079 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
2192011 TTAAATATGA
*
2192021 ATATATTTAATTTAAATTTTTAT
1 ATATATTTAAATTAAATTTTTAT
* *
2192044 ATAT-TTAAAAATTATATTTTTAT
1 ATATATT-TAAATTAAATTTTTAT
*
2192067 ATTTATTTTAAAT
1 ATATA-TTTAAAT
2192080 ATATATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 2 0.07
23 20 0.71
24 4 0.14
25 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATATTTAAATTAAATTTTTAT
Found at i:2192099 original size:36 final size:36
Alignment explanation
Indices: 2192001--2192099 Score: 87
Period size: 36 Copynumber: 2.7 Consensus size: 36
2191991 ATGTAGAATA
* *
2192001 TAAATATATATTAAATATGAATATATTTAATTTAAATTT
1 TAAATATATATTAAAT-TTAA-ATTTTTAATTT-AATTT
* * *
2192040 T-TATATAT-TTAAAAATTATATTTTTATATTT-ATTT
1 TAAATATATATT-AAATTTAAATTTTTA-ATTTAATTT
2192075 TAAATATATATTAAATTTAAATTTT
1 TAAATATATATTAAATTTAAATTTT
2192100 AAATATGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
35 5 0.10
36 23 0.48
37 10 0.21
38 9 0.19
39 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
TAAATATATATTAAATTTAAATTTTTAATTTAATTT
Found at i:2193992 original size:12 final size:11
Alignment explanation
Indices: 2193970--2194045 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
2193960 AGAGAAAGAA
*
2193970 GAGAGAGGAGG
1 GAGATAGGAGG
2193981 GATGATAGGAGG
1 GA-GATAGGAGG
*
2193993 AGAGACAGGA--
1 -GAGATAGGAGG
*
2194003 GAGATAGTA--
1 GAGATAGGAGG
2194012 GAGATAGGAGG
1 GAGATAGGAGG
2194023 GATGATAGGAGG
1 GA-GATAGGAGG
*
2194035 AGAGACAGGAG
1 -GAGATAGGAG
2194046 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:2194002 original size:24 final size:24
Alignment explanation
Indices: 2193969--2194054 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2193959 AAGAGAAAGA
*
2193969 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
2193993 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
2194011 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
2194035 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
2194055 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:2194021 original size:42 final size:42
Alignment explanation
Indices: 2193960--2194078 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
2193950 TAGCCCTCAA
* *
2193960 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
2194002 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2194044 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2194079 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2198024 original size:13 final size:12
Alignment explanation
Indices: 2198002--2198034 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2197992 TCAAATTTTT
2198002 TATTTT-TTAAAA
1 TATTTTATT-AAA
2198014 TATTTTATTAAA
1 TATTTTATTAAA
2198026 TATTTTATT
1 TATTTTATT
2198035 CATATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTTTATTAAA
Found at i:2198409 original size:2 final size:2
Alignment explanation
Indices: 2198402--2198429 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2198392 CTATAATGCA
2198402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2198430 GTATTCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2198907 original size:19 final size:21
Alignment explanation
Indices: 2198868--2198911 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
2198858 AATTCAATTT
2198868 AAATTATTATTTAAATAATAA
1 AAATTATTATTTAAATAATAA
2198889 AAATT-TTATTTAAAT-ATAA
1 AAATTATTATTTAAATAATAA
2198908 AAAT
1 AAAT
2198912 AATTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.35
20 10 0.43
21 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTATTATTTAAATAATAA
Found at i:2200073 original size:20 final size:21
Alignment explanation
Indices: 2200045--2200085 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2200035 GAAAATAATA
* *
2200045 AAAATAATTTTTAATT-TTTT
1 AAAACAATTATTAATTATTTT
2200065 AAAACAATTATTAATTATTTT
1 AAAACAATTATTAATTATTTT
2200086 TAATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AAAACAATTATTAATTATTTT
Found at i:2200655 original size:19 final size:21
Alignment explanation
Indices: 2200626--2200669 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2200616 TATATGGTAT
*
2200626 AAATTTATTTAT-TATTTTTA
1 AAATTTATTTATATATTTTAA
2200646 AAATTT-TTTATATATTTTAA
1 AAATTTATTTATATATTTTAA
2200666 AAAT
1 AAAT
2200670 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATTTATTTATATATTTTAA
Found at i:2200965 original size:21 final size:21
Alignment explanation
Indices: 2200905--2200967 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
2200895 TTTGATAAAG
* *
2200905 TGATATATTTATTAGATTAAA
1 TGATAAATTTATTAGATGAAA
*
2200926 TGATAAATTTATTAAATGAAA
1 TGATAAATTTATTAGATGAAA
* *
2200947 TGATACATTTATTGGATGAAA
1 TGATAAATTTATTAGATGAAA
2200968 AGATGCATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (21 bp):
TGATAAATTTATTAGATGAAA
Found at i:2201903 original size:2 final size:2
Alignment explanation
Indices: 2201896--2201936 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2201886 CCACCAAGTT
2201896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2201937 TGTATGGCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2202689 original size:4 final size:4
Alignment explanation
Indices: 2202680--2202706 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2202670 CACTCCAAAA
2202680 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2202707 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2204826 original size:22 final size:22
Alignment explanation
Indices: 2204801--2204844 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2204791 CTATTTGTTC
2204801 TCTTCGTTGTTATATTATAATA
1 TCTTCGTTGTTATATTATAATA
2204823 TCTTCGTTGTTATATTATAATA
1 TCTTCGTTGTTATATTATAATA
2204845 GTCCAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (22 bp):
TCTTCGTTGTTATATTATAATA
Found at i:2205172 original size:7 final size:7
Alignment explanation
Indices: 2205156--2205185 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2205146 AAAATACAAC
2205156 TTTT-TT
1 TTTTCTT
2205162 TTTTCTT
1 TTTTCTT
2205169 TTTTCTT
1 TTTTCTT
2205176 TTTTCTT
1 TTTTCTT
2205183 TTT
1 TTT
2205186 AATCCCGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:2206614 original size:3 final size:3
Alignment explanation
Indices: 2206608--2206636 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2206598 AAAAAAAATT
2206608 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2206637 CACTTTCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2211331 original size:2 final size:2
Alignment explanation
Indices: 2211324--2211373 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2211314 ATCTTTTCTG
2211324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2211366 AT AT AT AT
1 AT AT AT AT
2211374 TTAAATTCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2219709 original size:12 final size:12
Alignment explanation
Indices: 2219692--2219719 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2219682 TATATTTTTA
2219692 TTATATCATATT
1 TTATATCATATT
2219704 TTATATCATATT
1 TTATATCATATT
2219716 TTAT
1 TTAT
2219720 TTTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATCATATT
Found at i:2221564 original size:92 final size:93
Alignment explanation
Indices: 2221342--2221622 Score: 363
Period size: 92 Copynumber: 3.0 Consensus size: 93
2221332 TTCTCACAGC
* *
2221342 AAAAGGCTACCCAGATATAGCCACAAGGTACCGATAGTGTTCTCGAAGCCAAACCAGTTTCATGA
1 AAAAGGCTACCCAGATATAGCCACAAGGTATCGATAGTGTTTTCGAAGCCAAACCAGTTTCATGA
*
2221407 ATTTGCTTTAACCATTTTCTAGCTTATT
66 ATTTGCTTTAACCATTTTCTAGCTTATG
* * * *
2221435 TAAAGGCTACCCAGATATAGCCGC-AGGATATCCATAGTGTTTTTGAA-CGCAAACCAGTTTCAT
1 AAAAGGCTACCCAGATATAGCCACAAGG-TATCGATAGTGTTTTCGAAGC-CAAACCAGTTTCAT
* * *
2221498 AAATTTGC-TTGATCATTTTCTAGCTTATG
64 GAATTTGCTTTAACCATTTTCTAGCTTATG
* * * *
2221527 AAAAGGCTACCCAAATATAACCACAAGGTTTTGATAGTGTTTTCGAAGCCAAACCAGTTT-AGTG
1 AAAAGGCTACCCAGATATAGCCACAAGGTATCGATAGTGTTTTCGAAGCCAAACCAGTTTCA-TG
*
2221591 AATTTGCTTTAAACCATTCTCTAGCTTATG
65 AATTTGCTTT-AACCATTTTCTAGCTTATG
2221621 AA
1 AA
2221623 GCCTATTGTC
Statistics
Matches: 159, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
91 1 0.01
92 76 0.48
93 64 0.40
94 18 0.11
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (93 bp):
AAAAGGCTACCCAGATATAGCCACAAGGTATCGATAGTGTTTTCGAAGCCAAACCAGTTTCATGA
ATTTGCTTTAACCATTTTCTAGCTTATG
Found at i:2234718 original size:16 final size:16
Alignment explanation
Indices: 2234693--2234733 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2234683 TAAAAAAAAT
*
2234693 AATTAAAAATTAATTA
1 AATTATAAATTAATTA
*
2234709 AATTATAAA-TATTTA
1 AATTATAAATTAATTA
2234724 AATT-TAAATT
1 AATTATAAATT
2234734 TTAGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATAAATTAATTA
Found at i:2234741 original size:13 final size:14
Alignment explanation
Indices: 2234706--2234743 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2234696 TAAAAATTAA
2234706 TTAAATTATAAATAT
1 TTAAATT-TAAATAT
2234721 TTAAATTTAAAT-T
1 TTAAATTTAAATAT
*
2234734 TTAGATTTAA
1 TTAAATTTAA
2234744 TATCTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 5 0.23
15 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TTAAATTTAAATAT
Found at i:2235061 original size:16 final size:16
Alignment explanation
Indices: 2235021--2235062 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2235011 GTTTCGGATT
2235021 GGGTTATTTCGAGTTC
1 GGGTTATTTCGAGTTC
*
2235037 GGATTATTTCGAGTTC
1 GGGTTATTTCGAGTTC
*
2235053 GGGTCATTTC
1 GGGTTATTTC
2235063 AGATTCAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (16 bp):
GGGTTATTTCGAGTTC
Found at i:2236104 original size:26 final size:26
Alignment explanation
Indices: 2236074--2236132 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2236064 ACTAACTATC
2236074 TAAATTTTTTAAAACT-TTAAACAAAT
1 TAAATTTTTTAAAACTCTTAAA-AAAT
* *
2236100 TAAATTTTTTAAATCTCTTAAAATAT
1 TAAATTTTTTAAAACTCTTAAAAAAT
2236126 TAAATTT
1 TAAATTT
2236133 ATTTTGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATTTTTTAAAACTCTTAAAAAAT
Found at i:2239815 original size:2 final size:2
Alignment explanation
Indices: 2239810--2239845 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2239800 AAGATAAAAA
2239810 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2239846 CATATGAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2241674 original size:12 final size:12
Alignment explanation
Indices: 2241614--2241671 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
2241604 TTATTATTAT
2241614 TTTAAAATATTTA
1 TTTAAAAT-TTTA
*
2241627 TGTGTAATATTTATA
1 T-T-TAAAATTT-TA
*
2241642 TTTAATATTTTA
1 TTTAAAATTTTA
2241654 TTTAAAATTTT-
1 TTTAAAATTTTA
2241665 TTTAAAA
1 TTTAAAA
2241672 ATTAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 7 0.17
12 12 0.30
13 9 0.22
14 4 0.10
15 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTAAAATTTTA
Found at i:2242660 original size:22 final size:21
Alignment explanation
Indices: 2242633--2242673 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2242623 TAAATCTGAT
2242633 TGACTTAAACTTAAATTTAAAA
1 TGACTTAAACTT-AATTTAAAA
*
2242655 TGACTTGAACTTAATTTAA
1 TGACTTAAACTTAATTTAA
2242674 TCTAAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (21 bp):
TGACTTAAACTTAATTTAAAA
Found at i:2242811 original size:7 final size:8
Alignment explanation
Indices: 2242780--2242813 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
2242770 ACTTAAAAAT
2242780 AATTTTAA
1 AATTTTAA
2242788 AATTTTAA
1 AATTTTAA
2242796 AATTTTAA
1 AATTTTAA
2242804 AA-TTTAA
1 AATTTTAA
2242811 AAT
1 AAT
2242814 AACTTAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AATTTTAA
Found at i:2245538 original size:47 final size:47
Alignment explanation
Indices: 2245455--2245549 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
2245445 TCCAACATGA
2245455 AACCATCGTTGAAAGTTGGAAAATTTGAGCAAATCAATCAAATAGAC
1 AACCATCGTTGAAAGTTGGAAAATTTGAGCAAATCAATCAAATAGAC
* * * *
2245502 AACCATCGTTGAAAGTTGGGAACTTTGTGCAGATCAATCAAATAGAC
1 AACCATCGTTGAAAGTTGGAAAATTTGAGCAAATCAATCAAATAGAC
2245549 A
1 A
2245550 TTACATTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (47 bp):
AACCATCGTTGAAAGTTGGAAAATTTGAGCAAATCAATCAAATAGAC
Found at i:2245567 original size:2 final size:2
Alignment explanation
Indices: 2245560--2245595 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2245550 TTACATTTAC
2245560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2245596 GATTATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2245650 original size:29 final size:28
Alignment explanation
Indices: 2245621--2245718 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 28
2245611 AAAAAACAAT
2245621 ATTTTTAAATTTTATTATTTTATTTGAATAA
1 ATTTTTAAA-TTT-TTATTTTATTTGAAT-A
* **
2245652 ATTTTTATATTTTTATTTTATTAAAATA
1 ATTTTTAAATTTTTATTTTATTTGAATA
2245680 ATATTTT-AATTTTTAATTTATATTTAGAATAA
1 AT-TTTTAAATTTTT-ATTT-TATTT-GAAT-A
2245712 ATTTTTA
1 ATTTTTA
2245719 TTTTTTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
28 9 0.16
29 21 0.38
30 7 0.13
31 15 0.27
32 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTTTTAAATTTTTATTTTATTTGAATA
Found at i:2245676 original size:24 final size:23
Alignment explanation
Indices: 2245625--2245676 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2245615 AACAATATTT
2245625 TTAAATTTTATTATTTTATTTGA
1 TTAAATTTTATTATTTTATTTGA
* *
2245648 ATAAATTTT-TATATTTTTATTTTA
1 TTAAATTTTAT-TA-TTTTATTTGA
2245672 TTAAA
1 TTAAA
2245677 ATAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAAATTTTATTATTTTATTTGA
Found at i:2245712 original size:60 final size:60
Alignment explanation
Indices: 2245613--2245725 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
2245603 TTTTATTAAA
*
2245613 AAAACAATATTTTTAAATTTTATTATTTTATTTGAATAAATTTTTATATTTTTATTTTATT
1 AAAACAATATTTTTAAATTTTATAATTTTATTTGAATAAATTTTTAT-TTTTTATTTTATT
*
2245674 AAAATAATA-TTTT-AATTTT-TAATTTATATTTAGAATAAATTTTTATTTTTTA
1 AAAACAATATTTTTAAATTTTATAATTT-TATTT-GAATAAATTTTTATTTTTTA
2245726 ATTCTTATCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
58 5 0.10
59 17 0.35
60 18 0.38
61 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (60 bp):
AAAACAATATTTTTAAATTTTATAATTTTATTTGAATAAATTTTTATTTTTTATTTTATT
Found at i:2245760 original size:61 final size:58
Alignment explanation
Indices: 2245637--2245781 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 58
2245627 AAATTTTATT
* *
2245637 ATTT-TATTT-GAATAAATTTTTATATTTTTATTTTATTAAAATAATATTTTAATTTTTA
1 ATTTATATTTAGAATAAATTTTTAT-TTTTTATTTTATCAAAATAATA-TTTAATCTTTA
*
2245695 ATTTATATTTAGAATAAATTTTTATTTTTTAATTCTTATCCAAATCAATCA-TTAATCTTTA
1 ATTTATATTTAGAATAAATTTTTATTTTTT-ATT-TTATCAAAAT-AAT-ATTTAATCTTTA
** *
2245756 ATTTATAAATA-AATTAATTTTTATTT
1 ATTTATATTTAGAATAAATTTTTATTT
2245782 AAAAAAATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
58 4 0.05
59 10 0.13
60 31 0.41
61 26 0.35
62 3 0.04
63 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (58 bp):
ATTTATATTTAGAATAAATTTTTATTTTTTATTTTATCAAAATAATATTTAATCTTTA
Found at i:2245771 original size:23 final size:20
Alignment explanation
Indices: 2245745--2245790 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
2245735 CAAATCAATC
2245745 ATTAATCTTTAATTTATAAATAA
1 ATTAAT-TTTAATTTA-AAA-AA
*
2245768 ATTAATTTTTATTTAAAAAA
1 ATTAATTTTAATTTAAAAAA
2245788 ATT
1 ATT
2245791 TTATTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 8 0.36
23 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAATTTTAATTTAAAAAA
Found at i:2246195 original size:2 final size:2
Alignment explanation
Indices: 2246188--2246223 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2246178 TATAAAATAG
*
2246188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2246224 ACAAACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2246493 original size:19 final size:21
Alignment explanation
Indices: 2246469--2246521 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2246459 CATTTTAAAA
2246469 ATATTAAAATTT-TAT-TTTT
1 ATATTAAAATTTATATATTTT
*
2246488 ATATTAATATTTATATATTTT
1 ATATTAAAATTTATATATTTT
2246509 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
2246522 AGTAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 12 0.41
22 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAAATTTATATATTTT
Found at i:2247180 original size:27 final size:27
Alignment explanation
Indices: 2247121--2247193 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
2247111 TTCAATTCGA
*
2247121 ATTATTATTT-AA-TAAAT-AAAATTT
1 ATTATTATTTAAATTAAATAAAAATAT
*
2247145 ATTTTTATTTAAATTAAATAAAAATAT
1 ATTATTATTTAAATTAAATAAAAATAT
* *
2247172 ATTAATA-TTAATATTTAATAAA
1 ATTATTATTTAA-ATTAAATAAA
2247194 TTTTAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 9 0.22
25 2 0.05
26 9 0.22
27 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTATTATTTAAATTAAATAAAAATAT
Found at i:2257100 original size:15 final size:14
Alignment explanation
Indices: 2257077--2257119 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2257067 AAAAAAAAAC
2257077 TTTTTTAATTAATT
1 TTTTTTAATTAATT
* *
2257091 TTTTTATAATAAAAT
1 TTTTT-TAATTAATT
2257106 TTTTTTAATTAATT
1 TTTTTTAATTAATT
2257120 ATATAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTAATTAATT
Found at i:2257128 original size:29 final size:29
Alignment explanation
Indices: 2257072--2257140 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2257062 CAAAAAAAAA
* * * *
2257072 AAAACTTTTTTAATTAATTTTTTTATAAT
1 AAAATTTTTTTAATTAATTATATAATAAT
2257101 AAAATTTTTTTAATTAATTATATAATAAT
1 AAAATTTTTTTAATTAATTATATAATAAT
*
2257130 ACATATTTTTT
1 A-AAATTTTTT
2257141 CCGAGATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
AAAATTTTTTTAATTAATTATATAATAAT
Found at i:2257548 original size:23 final size:22
Alignment explanation
Indices: 2257518--2257560 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2257508 AAATTTAAAT
*
2257518 AAATAAAAATATTTTTAAAATAA
1 AAATAAAAAT-TATTTAAAATAA
2257541 AAATAAAAATTATTTAAAAT
1 AAATAAAAATTATTTAAAAT
2257561 TTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAAAAATTATTTAAAATAA
Found at i:2257895 original size:26 final size:27
Alignment explanation
Indices: 2257866--2257935 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
2257856 TAGCAAGTTT
2257866 TTAATATTTATAAATATTTA-ATTAAA
1 TTAATATTTATAAATATTTACATTAAA
* *
2257892 TTAATAATTA-AATAAATTTACATTAAA
1 TTAATATTTATAA-ATATTTACATTAAA
2257919 TT-ATATTATATTAAATA
1 TTAATATT-TA-TAAATA
2257936 ATTATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.06
26 19 0.54
27 10 0.29
28 2 0.06
29 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAATATTTATAAATATTTACATTAAA
Found at i:2257951 original size:19 final size:19
Alignment explanation
Indices: 2257918--2257976 Score: 100
Period size: 19 Copynumber: 3.0 Consensus size: 19
2257908 TTTACATTAA
2257918 ATTATATTATATTAAATAATT
1 ATTAT-TTAT-TTAAATAATT
2257939 ATTATTTATTTAAATAATT
1 ATTATTTATTTAAATAATT
2257958 ATTATTTATTTAAATAATT
1 ATTATTTATTTAAATAATT
2257977 TTTTGCATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 29 0.76
20 4 0.11
21 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTTATTTAAATAATT
Found at i:2258712 original size:13 final size:13
Alignment explanation
Indices: 2258691--2258736 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2258681 ACATTATACA
*
2258691 AAAAGAATATAAAT
1 AAAA-AATAAAAAT
2258705 AAAAAATAAAAAT
1 AAAAAATAAAAAT
* *
2258718 ATAATATAAAAAT
1 AAAAAATAAAAAT
2258731 AAAAAA
1 AAAAAA
2258737 AATAAATATG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:2258720 original size:19 final size:19
Alignment explanation
Indices: 2258696--2258735 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
2258686 ATACAAAAAG
2258696 AATATAA-ATAAAAAATAAA
1 AATATAATAT-AAAAATAAA
2258715 AATATAATATAAAAATAAA
1 AATATAATATAAAAATAAA
2258734 AA
1 AA
2258736 AAATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AATATAATATAAAAATAAA
Found at i:2258756 original size:22 final size:22
Alignment explanation
Indices: 2258688--2258759 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
2258678 GAAACATTAT
*
2258688 ACAAAAAGAATATAA-AT-AAA
1 ACAAAAAAAATATAATATAAAA
*
2258708 A-AATAAAAATATAATATAAAA
1 ACAAAAAAAATATAATATAAAA
* *
2258729 ATAAAAAAAATA-AATATGACAA
1 ACAAAAAAAATATAATAT-AAAA
2258751 ACAAAAAAA
1 ACAAAAAAA
2258760 TGCAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.26
20 3 0.07
21 9 0.21
22 20 0.47
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (22 bp):
ACAAAAAAAATATAATATAAAA
Found at i:2259025 original size:22 final size:23
Alignment explanation
Indices: 2258996--2259056 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
2258986 TATGATCTAA
2258996 ATAATATAGAATATTAAAAAAAT
1 ATAATATAGAATATTAAAAAAAT
2259019 -TAATATAGAATA-TAAATAAAAT
1 ATAATATAGAATATTAAA-AAAAT
2259041 ATAA-A-A-AATATTAAAA
1 ATAATATAGAATATTAAAA
2259057 TATTATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.14
21 9 0.26
22 18 0.51
23 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAATATAGAATATTAAAAAAAT
Found at i:2259065 original size:33 final size:33
Alignment explanation
Indices: 2258996--2259067 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
2258986 TATGATCTAA
* *
2258996 ATAATATAGAATATTAAAAAAATTAATATAGAAT
1 ATAA-ATAAAATATTAAAAAAATTAAAATAGAAT
**
2259030 ATAAATAAAATA-TAAAAAATATTAAAATATTAT
1 ATAAATAAAATATTAAAAAA-ATTAAAATAGAAT
2259063 ATAAA
1 ATAAA
2259068 AATAGCATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 7 0.21
33 22 0.67
34 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAATAAAATATTAAAAAAATTAAAATAGAAT
Found at i:2259381 original size:26 final size:28
Alignment explanation
Indices: 2259326--2259400 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 28
2259316 AAAATATAAA
* *
2259326 ATAAATTAAAATATTATACAAACACAAC
1 ATAAATAAAAATAATATACAAACACAAC
2259354 ATAAATAAAAATAAT-TA-AAACACAAC
1 ATAAATAAAAATAATATACAAACACAAC
2259380 ATAAA-AATAATATAA-ATACAA
1 ATAAATAA-AA-ATAATATACAA
2259401 CATAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 2 0.05
26 16 0.39
27 8 0.20
28 15 0.37
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.23
Consensus pattern (28 bp):
ATAAATAAAAATAATATACAAACACAAC
Found at i:2259383 original size:22 final size:22
Alignment explanation
Indices: 2259358--2259405 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2259348 CACAACATAA
2259358 ATAAAAATAAT-TAAAACACAAC
1 ATAAAAATAATAT-AAACACAAC
*
2259380 ATAAAAATAATATAAATACAAC
1 ATAAAAATAATATAAACACAAC
2259402 ATAA
1 ATAA
2259406 TTATACGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (22 bp):
ATAAAAATAATATAAACACAAC
Found at i:2259516 original size:20 final size:21
Alignment explanation
Indices: 2259465--2259523 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
2259455 ATAATATTTT
2259465 AAAT-ATATAAAAAATAATATA
1 AAATAATAT-AAAAATAATATA
*
2259486 AATACAATATAAAAATAAT-TA
1 AA-ATAATATAAAAATAATATA
*
2259507 AAATAATATAAGAATAA
1 AAATAATATAAAAATAA
2259524 ATATGACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
22 10 0.30
23 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATATAAAAATAATATA
Found at i:2260157 original size:2 final size:2
Alignment explanation
Indices: 2260150--2260174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2260140 ATCAAAACTA
2260150 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2260175 AATGCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2260439 original size:24 final size:23
Alignment explanation
Indices: 2260412--2260463 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2260402 AAATTATTTA
*
2260412 AAATAATTTTTATACATTAATAA-T
1 AAATAAATTTTATA-ATTAA-AATT
2260436 AAATTAAATTTTATAATTAAAATT
1 AAA-TAAATTTTATAATTAAAATT
2260460 AAAT
1 AAAT
2260464 TATATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.12
24 12 0.48
25 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAAATTTTATAATTAAAATT
Found at i:2260464 original size:24 final size:26
Alignment explanation
Indices: 2260409--2260465 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
2260399 ATTAAATTAT
* *
2260409 TTAAAATAATTTTTATACATTAATAA
1 TTAAATTAAATTTTATACATTAATAA
2260435 -TAAATTAAATTTTATA-ATTAA-AA
1 TTAAATTAAATTTTATACATTAATAA
2260458 TTAAATTA
1 TTAAATTA
2260466 TATCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 12 0.43
25 14 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAATTAAATTTTATACATTAATAA
Found at i:2260677 original size:20 final size:19
Alignment explanation
Indices: 2260630--2260677 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2260620 TGTTAGTATT
*
2260630 TATAT-TATTTTTATTTAA
1 TATATATATTTTTATATAA
*
2260648 AATATGATATTTTTATATATA
1 TATAT-ATATTTTTATATA-A
2260669 TATATATAT
1 TATATATAT
2260678 ATGTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
20 15 0.62
21 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATATATTTTTATATAA
Done.